Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice

Authors

  • Manuel R. Teixeira Serviço de Genética. Instituto Português de Oncologia do Porto Francisco Gentil. Porto. Instituto de Ciências Biomédicas Abel Salazar. Universidade do Porto. Porto.
  • Júlio Oliveira Serviço de Oncologia Médica. Instituto Português de Oncologia do Porto Francisco Gentil. Porto.
  • Paula Borralho Serviço de Anatomia Patológica. Hospital CUF Descobertas. Lisboa. Faculdade de Medicina. Universidade de Lisboa. Lisboa.
  • Maria Gabriela O. Fernandes Serviço de Pneumologia. Centro Hospitalar Universitário de São João. Porto. Departamento de Medicina. Faculdade de Medicina. Universidade do Porto. Porto. Institute of Molecular Pathology and Immunology. University of Porto. Porto.
  • Teresa Almodovar Serviço de Pneumologia. Instituto Português de Oncologia de Lisboa Francisco Gentil. Lisboa.
  • Isabel Fernandes Faculdade de Medicina. Universidade de Lisboa. Lisboa. Serviço de Oncologia Médica. Centro Hospitalar Universitário de Lisboa Norte. Lisboa. Instituto de Medicina Molecular João Lobo Antunes. Faculdade de Medicina. Universidade de Lisboa. Lisboa.
  • Daniela Macedo Centro de Oncologia. Hospital Lusíadas Lisboa. Lisboa.
  • Ana Ferreira Serviço de Oncologia Médica. Instituto Português de Oncologia do Porto Francisco Gentil. Porto.
  • Ana Barroso Unidade Multidisciplinar de Tumores Torácicos. Serviço de Pneumologia. Centro Hospitalar de Vila Nova de Gaia/Espinho. Vila Nova de Gaia.
  • Encarnação Teixeira Serviço de Pneumologia. Centro Hospitalar Universitário de Lisboa Norte. Lisboa. Serviço de Pneumologia. Hospital CUF Descobertas. Lisboa. Serviço de Pneumologia. Hospital CUF Tejo. Lisboa.
  • José Carlos Machado Institute of Molecular Pathology and Immunology. University of Porto. Porto. Departamento de Patologia. Faculdade de Medicina. Universidade do Porto. Porto. https://orcid.org/0000-0003-4741-8415

DOI:

https://doi.org/10.20344/amp.17680

Keywords:

High-Throughput Nucleotide Sequencing, Lung Neoplasms/genetics, Neoplasms, Unknown Primary/genetics, Sarcoma/genetics

Abstract

Next-generation sequencing (NGS) has been implemented in clinical oncology for diagnosis, prognosis, and therapeutic guidance. Among the various NGS applications in molecular oncology, we focused on the following topics: laboratory standards for targeted gene panels (somatic mutations) and therapeutic guidance based on NGS of lung cancer and rare cancers, namely sarcomas and cancers of unknown primary. Multiple quality control checkpoints should be addressed in the pre-analytical phase for good quality and interpretation of the NGS results. It includes tumor size and cellularity, tissue processing and decalcification, tumor fraction, tumor viability, fixatives, and staining. Communication between clinicians and laboratory support is also essential. In lung cancer, all patients with non-squamous non-small cell lung cancer should be tested with a NGS panel, and it should include not only genes with approved targeted therapies (ALK, BRAF, EGFR, MET, NTRK, RET, and ROS1) but also genes with potentially actionable genomic alterations (HER2 and KRAS). Since there is a lack of extensive knowledge regarding the use of NGS in rare tumors performing comprehensive genomic profiling, NGS panels to better manage the disease are recommended. Moreover, other patients with other incurable solid tumors may benefit from being included in biomarker-driven clinical trials. Multidisciplinary tumor boards with the participation of experts with the ability to integrate genomic profiling data are essential to tailor the best strategy for each patient. Considering that there are no national guidelines, this article aims to guide laboratory and clinical practice for the use of NGS in the context of lung cancer, rare tumors, and cancer of unknown primary in Portugal.

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Published

2022-09-01

How to Cite

1.
R. Teixeira M, Oliveira J, Borralho P, O. Fernandes MG, Almodovar T, Fernandes I, Macedo D, Ferreira A, Barroso A, Teixeira E, Machado JC. Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice. Acta Med Port [Internet]. 2022 Sep. 1 [cited 2022 Dec. 1];35(9):677-90. Available from: https://www.actamedicaportuguesa.com/revista/index.php/amp/article/view/17680

Issue

Section

Guidelines